.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/01_DataOperations/plot_neurovault_io.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_01_DataOperations_plot_neurovault_io.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_01_DataOperations_plot_neurovault_io.py:

Neurovault I/O
==============

Data can be easily downloaded and uploaded to `neurovault <http://neurovault.org/>`_
using `pynv <https://github.com/neurolearn/pynv>`_, a python wrapper for the
neurovault api.

.. GENERATED FROM PYTHON SOURCE LINES 12-20

Download a Collection
---------------------

Entire collections from neurovault can be downloaded along with the
accompanying image metadata.  You just need to know the collection ID.
Data will be downloaded to the path specified in the 'data_dir' flag 
or '~/nilearn_data' by default.  These files can then be imported into
nltools as a Brain_Data() instance.

.. GENERATED FROM PYTHON SOURCE LINES 20-27

.. code-block:: default


    from nltools.datasets import download_collection
    from nltools.data import Brain_Data

    metadata,files = download_collection(collection=2099)
    mask = Brain_Data(files,X=metadata)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    Dataset created in /home/runner/nilearn_data/2099

    Downloading data from http://neurovault.org/media/images/2099/Neurosynth%20Parcellation_0.nii.gz ...
     ...done. (0 seconds, 0 min)
    Downloading data from http://neurovault.org/media/images/2099/Neurosynth%20Parcellation_1.nii.gz ...
     ...done. (0 seconds, 0 min)
    Downloading data from http://neurovault.org/media/images/2099/Neurosynth%20Parcellation_2.nii.gz ...
     ...done. (0 seconds, 0 min)




.. GENERATED FROM PYTHON SOURCE LINES 28-36

Download a Single Image from the Web
------------------------------------

It's possible to load a single image from a web URL using the Brain_Data 
load method.  The files are downloaded to a temporary directory and will 
eventually be erased by your computer so be sure to write it out to a file 
if you would like to save it.  Here we plot it using nilearn's glass brain
function.

.. GENERATED FROM PYTHON SOURCE LINES 36-43

.. code-block:: default


    from nilearn.plotting import plot_glass_brain

    mask = Brain_Data('http://neurovault.org/media/images/2099/Neurosynth%20Parcellation_0.nii.gz')

    plot_glass_brain(mask.to_nifti())




.. image-sg:: /auto_examples/01_DataOperations/images/sphx_glr_plot_neurovault_io_001.png
   :alt: plot neurovault io
   :srcset: /auto_examples/01_DataOperations/images/sphx_glr_plot_neurovault_io_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f377bc94520>



.. GENERATED FROM PYTHON SOURCE LINES 44-53

Upload Data to Neurovault
-------------------------

There is a method to easily upload a Brain_Data() instance to 
`neurovault <http://neurovault.org>`_.  This requires using your api key, which can be found
under your account settings.  Anything stored in data.X will be uploaded as
image metadata.  The required fields include collection_name, the img_type,
img_modality, and analysis_level.  See https://github.com/neurolearn/pyneurovault_upload
for additional information about the required fields.  (Don't forget to uncomment the line!)

.. GENERATED FROM PYTHON SOURCE LINES 53-59

.. code-block:: default


    api_key = 'your_neurovault_api_key'

    # mask.upload_neurovault(access_token=api_key, collection_name='Neurosynth Parcellation', 
    #                        img_type='Pa', img_modality='Other',analysis_level='M')









.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 4.543 seconds)


.. _sphx_glr_download_auto_examples_01_DataOperations_plot_neurovault_io.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example




    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_neurovault_io.py <plot_neurovault_io.py>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_neurovault_io.ipynb <plot_neurovault_io.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_